Readd init files

src/sage/__init__.py

@@ -0,0 +1,2 @@
+# This is only here to mark the sage directory as a Python package
+# (so that cython determines the correct module name)

src/sage/algebras/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/algebras/finite_dimensional_algebras/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/algebras/fusion_rings/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/algebras/hecke_algebras/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/algebras/letterplace/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/algebras/lie_algebras/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/algebras/lie_conformal_algebras/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/algebras/quantum_groups/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/algebras/quatalg/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/algebras/steenrod/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/arith/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/calculus/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/calculus/transforms/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/categories/examples/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/coding/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/coding/codecan/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/coding/guruswami_sudan/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/coding/source_coding/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/combinat/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/combinat/chas/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/combinat/cluster_algebra_quiver/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/combinat/crystals/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/combinat/designs/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/combinat/matrices/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/combinat/ncsf_qsym/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/combinat/ncsym/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/combinat/path_tableaux/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/combinat/posets/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/combinat/rigged_configurations/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/combinat/root_system/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/combinat/sf/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/combinat/species/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/combinat/words/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/crypto/block_cipher/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/crypto/public_key/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/data_structures/__init__.py

@@ -0,0 +1 @@
+# So that cython creates the correct module names

src/sage/databases/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/dynamics/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/dynamics/arithmetic_dynamics/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/dynamics/cellular_automata/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/dynamics/complex_dynamics/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/ext/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/functions/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/game_theory/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/games/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/geometry/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/geometry/hyperbolic_space/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/geometry/hyperplane_arrangement/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/geometry/polyhedron/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/geometry/polyhedron/combinatorial_polyhedron/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/geometry/polyhedron/modules/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/geometry/riemannian_manifolds/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/geometry/triangulation/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/graphs/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/graphs/base/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/graphs/generators/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/graphs/graph_decompositions/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/groups/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/groups/abelian_gps/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/groups/additive_abelian/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/groups/affine_gps/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/groups/lie_gps/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/groups/matrix_gps/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/groups/misc_gps/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/groups/perm_gps/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/groups/perm_gps/partn_ref/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/groups/perm_gps/partn_ref2/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/groups/semimonomial_transformations/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/homology/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/interacts/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/interfaces/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/knots/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/lfunctions/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/libs/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/libs/gap/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/libs/mpc/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/libs/mpfi/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/libs/mpfr/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/libs/polybori/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/logic/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/manifolds/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/manifolds/differentiable/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/manifolds/differentiable/examples/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/manifolds/subsets/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/matrix/__init__.py

@@ -0,0 +1 @@
+# Because of relative imports

src/sage/matroids/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/misc/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/misc/cython.py

@@ -22,16 +22,14 @@
 import builtins
 import os
 import re
-import sys
 import shutil
+import sys
 
-from sage.env import (SAGE_LOCAL, cython_aliases,
-                      sage_include_directories)
+from sage.env import SAGE_LOCAL, cython_aliases, sage_include_directories
+from sage.misc.cachefunc import cached_function
+from sage.misc.sage_ostools import redirection, restore_cwd
 from sage.misc.temporary_file import spyx_tmp, tmp_filename
 from sage.repl.user_globals import get_globals
-from sage.misc.sage_ostools import restore_cwd, redirection
-from sage.cpython.string import str_to_bytes
-from sage.misc.cachefunc import cached_function
 
 
 @cached_function
@@ -227,16 +225,13 @@ def cython(filename, verbose=0, compile_message=False,
         ....: ''')
 
     In Cython 0.29.33 using `from PACKAGE cimport MODULE` is broken
-    when `PACKAGE` is a namespace package, see :issue:`35322`::
+    when `PACKAGE` is a namespace package, see :issue:`35322`
+    (but as of now sage.misc is not a namespace package, so this passes)::
 
         sage: cython('''
         ....: from sage.misc cimport cachefunc
         ....: ''')
-        Traceback (most recent call last):
-        ...
-        RuntimeError: Error compiling Cython file:
-        ...
-        ...: 'sage/misc.pxd' not found
+
     """
     if not filename.endswith('pyx'):
         print("Warning: file (={}) should have extension .pyx".format(filename), file=sys.stderr)
@@ -318,18 +313,18 @@ def cython(filename, verbose=0, compile_message=False,
     includes = [os.getcwd()] + standard_includes
 
     # Now do the actual build, directly calling Cython and distutils
+    import Cython.Compiler.Options
     from Cython.Build import cythonize
     from Cython.Compiler.Errors import CompileError
-    import Cython.Compiler.Options
 
     try:
         from setuptools.dist import Distribution
         from setuptools.extension import Extension
     except ImportError:
         # Fall back to distutils (stdlib); note that it is deprecated
         # in Python 3.10, 3.11; https://www.python.org/dev/peps/pep-0632/
-        from distutils.dist import Distribution
         from distutils.core import Extension
+        from distutils.dist import Distribution
 
     from distutils.log import set_verbosity
     set_verbosity(verbose)

src/sage/modular/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/modular/abvar/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/modular/arithgroup/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/modular/btquotients/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/modular/hecke/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/modular/local_comp/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/modular/modform/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/modular/modform_hecketriangle/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/modular/modsym/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/modular/overconvergent/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/modular/pollack_stevens/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/modular/quasimodform/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/modular/quatalg/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/modular/ssmod/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/modules/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/modules/fg_pid/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/modules/fp_graded/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/modules/fp_graded/steenrod/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/modules/with_basis/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/monoids/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/numerical/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/numerical/backends/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/parallel/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/plot/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/plot/plot3d/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/probability/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/quadratic_forms/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/quadratic_forms/genera/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/quivers/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/rings/__init__.py

@@ -0,0 +1 @@
+# To make cython create the correct module name

src/sage/rings/asymptotic/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/rings/convert/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/rings/finite_rings/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/rings/function_field/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/rings/function_field/drinfeld_modules/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/rings/invariants/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/rings/number_field/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/rings/padics/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/rings/polynomial/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/rings/polynomial/padics/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/rings/polynomial/weil/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/rings/semirings/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/rings/valuation/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/sandpiles/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/sat/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/schemes/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/schemes/affine/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/schemes/berkovich/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/schemes/curves/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/schemes/cyclic_covers/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/schemes/elliptic_curves/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/schemes/generic/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/schemes/hyperelliptic_curves/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/schemes/jacobians/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/schemes/plane_conics/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/schemes/plane_quartics/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/schemes/product_projective/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/schemes/projective/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/schemes/riemann_surfaces/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/schemes/toric/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/schemes/toric/sheaf/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/sets/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/stats/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/stats/distributions/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/stats/hmm/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/symbolic/__init__.py

@@ -0,0 +1 @@
+# here so that cython creates the correct module name

src/sage/symbolic/integration/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/tensor/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/tensor/modules/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/tests/books/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/topology/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage/typeset/__init__.py

@@ -0,0 +1 @@
+# Here so that cython creates the correct module name

src/sage_setup/autogen/interpreters/__init__.py

@@ -226,11 +226,6 @@ def rebuild(dirname, force=False, interpreters=None, distribution=None):
     except OSError:
         if not os.path.isdir(dirname):
             raise
-        # Remove leftover file from before move to namespace packages
-        try:
-            os.remove(os.path.join(dirname, '__init__.py'))
-        except FileNotFoundError:
-            pass
 
     # Although multiple files are generated by this function, since
     # they are all generated at once it suffices to make sure if just